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The U.S. Constitution's "Commerce Clause" (Article I, Section 8) grants the federal government authority to regulate interstate commerce. The same section contains the "Taxing and Spending Clause" which grants the federal government authority to "lay and collect taxes, duties, imposts and excises, to pay the debts and provide for the common defense and general welfare of the United States."

Has federal law drawn a line on what taxes, duties, etc., can be collected by the states?

Evidently the states can tax (a) income and property of citizens and entities within their borders; (b) commerce (via sales and excise taxes) conducted within their borders. Has any restraint been imposed on such taxation, other than the prohibition on double-taxation affirmed in Comptroller of the Treasury of Maryland v. Wynne (SCOTUS, 2015)?

One prohibition I suspect exists, but I can't find in law: Can states impose duties on goods that merely transit their territory?

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Are there any restrictions on the taxes or duties a U.S. state can levy?

Yes. For starters, states may not use taxes or other means to impede the federal government in its constitutional exercises of power. This precedent stems from a case called McCulloch v. Maryland from 1819. In 1816, Congress established the Second Bank of the United States. Many states were not fans of this action. One of them, Maryland, established a tax on all notes of banks not chartered in Maryland. When the head of the Baltimore branch of the bank refused to pay the tax, litigation commenced and it was eventually appealed to the Supreme Court. SCOTUS held that the Constitution grants implied powers to Congress that allow Congress to implement a national government using its express powers and state action may not interfere with such exercise of power. Taxation, of course, is just one way a state may attempt to interfere with federal power.

Can states impose duties on goods that merely transit their territory?

Generally no. The Commerce Clause bars states from implementing taxes that discriminate against interstate commerce or that put burdens on it by subjecting commercial activities to numerous or unfair taxation. The Due Process Clause complements this concept by requiring there be a definitive link between a state and the person, property, or transaction which it seeks to tax. This goes back to the SCOTUS decision in Southern Pacific Co. v. Arizona where the state enacted a law barring trains from operating in the state with more than 14 or 70 passenger or freight cars, respectively. The Court held that this was a substantial burden on interstate commerce because trains would need to be broken up before they passed through AZ. Also, you couldn't just stop on the tracks and "break up" the trains, so that had to be done at a stop before getting to AZ. The court determined that with this law, AZ effectively controlled the length of trains as far from its borders as El Paso and Los Angeles. The alternative was to operate all trains at the lowest level allowable by any state, which would lead to AZ dictating train lengths around the country. In determining the validity of the law or regulation, a court uses a balancing test to compare the burden on interstate commerce with the importance of the state interest (the AZ law was purportedly for safety reasons).

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There are at least five main federal limitations on state taxation, in addition to those imposed under state constitutions. Subject to these limitations, the power of states to impose taxes is plenary (i.e. unlimited).

Jurisdiction To Tax Activity Within And Outside A State

Evidently the states can tax (a) income and property of citizens and entities within their borders; (b) commerce (via sales and excise taxes) conducted within their borders. Has any restraint been imposed on such taxation, other than the prohibition on double-taxation affirmed in Comptroller of the Treasury of Maryland v. Wynne (SCOTUS, 2015)?

To impose a tax, a state must have constitutional taxing jurisdiction over the transaction or activity taxed. This question mentions a couple of examples, but there is another big basis for taxing jurisdiction that is omitted.

States can tax mail order/Internet purchases delivered to their state under a recent U.S. Supreme Court ruling, South Dakota v. Wayfair, Inc., 585 U.S. ___ (2018), overturning prior prohibitions on that practice articulated in its 1992 ruling in Quill Corp. v. North Dakota. A complex set of state laws followed, and so far, these state laws have not been harmonized with a federal statute or interstate compact.

Duties On Goods Transiting A State's Territory

One prohibition I suspect exists, but I can't find in law: Can states impose duties on goods that merely transit their territory?

Yes. They can impose duties on goods that merely transit their territory, although, to be more exact, this is limited to inspection fees and to road use taxes based upon weight and not value.

The main U.S. Constitutional restrictions on state taxation powers are in clauses 2-3 of Section 10 of Article I which says:

Clause 2 – Taxes on imports and exports restricted

No state shall, without the consent of the Congress, lay any imposts or duties on imports or exports, except what may be absolutely necessary for executing its inspection laws; and the net produce of all duties and imposts, laid by any state on imports or exports, shall be for the use of the treasury of the United States; and all such laws shall be subject to the revision and control of the Congress.

Clause 3 – Other conditional restrictions

No state shall, without the consent of Congress, lay any duty of tonnage; keep troops or ships of war in time of peace; enter into any agreement or compact with another state, or with a foreign power; or engage in war, unless actually invaded or in such imminent danger as will not admit of delay.

It is, in fact, routine, for this to be done in the case of semis engaged in long haul trucking which is why you see "weigh stations" along every major highway, because states can tax the use of their roads which is a form of commerce conducted in their states. Historically, this was done on a state by state individualized basis, but now there is an interstate compact, known as the IFTA, to which the lower 48 states and most provinces of Canada are a part, to which Congress has consented, governing how this is done. In practice, all of Canada, and every state except Hawaii, which for mysterious reasons doesn't have a lot of highway traffic from other states, participates.

Dormant Commerce Clause Restrictions

But, this power is limited by a doctrine known as the "dormant commerce clause" (a.k.a. the "negative commerce clause") that constitutionally invalidates state regulations that impose an undue burden on interstate commerce under an analysis similar to that used to determine if a state law is pre-empted by a federal law under the Supremacy Clause of the U.S. Constitution at Article IV, Section 1, Clause 2 which states that:

Clause 2 – Supreme law of the land

This Constitution, and the laws of the United States which shall be made in pursuance thereof, and all treaties made, or which shall be made, under the authority of the United States, shall be the supreme law of the land; and the judges in every state shall be bound thereby, anything in the constitution or laws of any state to the contrary notwithstanding.

One of the leading dormant commerce clause cases is cited by @A.fm. in another answer to this question:

Southern Pacific Company v. Arizona, 325 U.S. 761 (1945), was a United States Supreme Court case in which the Court held that the Arizona Train Limit Law of 1912, which prohibited passenger trains with more than fourteen cars and prohibited freight trains with more than seventy cars, placed an unconstitutional burden on interstate commerce.1 The Court held that the law imposed a burden far greater than necessary to achieve Arizona's legitimate interest in lowering the rate of train accidents. This case is part of the Court's so-called negative commerce clause jurisprudence.

Prohibitions On State Citizenship Discrimination

Also relevant is Article I, Section 2, Clause 1 which states:

Clause 1 – Privileges of citizenship

The citizens of each state shall be entitled to all privileges and immunities of citizens in the several states.

This bars inferior treatment of persons from out of state (although it is not absolute). For example, a state cannot impose different sales tax rates on stores owned by people from another U.S. state relative to locally owned stores.

Prohibitions On Federal Entity Discrimination

McCulloch v. Maryland (1819) established, on federalism grounds, that federally chartered entities and the federal government cannot be discriminated against in state taxation.

In general, the federal government and its property cannot be taxed at all by states, but, for example, the income of federal employees and income from federal bond interest and federal contracts, can be taxed on a non-discriminatory basis.

In some circumstances where a local government is heavily impacted, the federal government voluntarily pays local governments an amount in lieu of local property taxes that it would otherwise owe.

Taxes Impairing Constitutional Rights

Also, a state may not impose a tax that infringes on a constitutional right. The leading cases barred a tax that was limited to newspapers as a burden on the First Amendment free press right. Some the of case law is as follows:

The leading case in this area of law is Grosjean v. American Press Co. (1936). A unanimous U.S. Supreme Court struck down a 2 percent license tax that the state of Louisiana— then largely dominated politically by its former governor and then U.S. senator, Huey Long—had imposed on the gross receipts of newspapers with circulations of more than 20,000 copies a week. The Court recognized that it was no coincidence that the tax fell largely on those newspapers critical of Long and his political allies. In writing the Court’s decision, Justice George Sutherland observed that newspapers were not “immune from any of the ordinary forms of taxation for support of the government” but also pointed out the dangers of differential taxation.

The Court reiterated this position in Minneapolis Star and Tribune Co. v. Minnesota Commissioner of Revenue (1983) when it struck down a Minnesota “use tax” on the cost of paper and products used by periodicals in excess of $100,000 a year. Because there were only eleven publishers—including the Minneapolis Star Tribune—that fit this description, Justice Sandra Day O’Connor feared that the tax was “facially discriminatory.”

Justice Thurgood Marshall came to a similar conclusion in writing the Court’s decision in Arkansas Writers’ Project, Inc. v. Ragland (1987). In this case, the Court overturned an Arkansas law that exempted some specialty publications from the state’s sale tax but not general interest magazines like the Arkansas Times. Marshall observed that “a power to tax differentially,as opposed to a power to tax generally, gives a government a powerful weapon against the taxpayer selected.” By contrast, Justice Antonin Scalia, joined by Chief Justice William H. Rehnquist, expressed the minority view that the state plan was little different from other subsidies that the Court had upheld.

This analysis would also apply, for example, to taxes infringing on the constitutional right to access to an abortion or contraception.

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