Former secretary of state George Shultz used to compare diplomacy to tending a garden. If you wanted results, you had to keep up with it.

As the secretary of state lands in Israel this week, she will see a lot more weeds than flowers. And no amount of watering and weeding is going to make this garden grow, whether on the peace process, Iran or the Bibi-Obama relationship. Rarely has a secretary of state been more boxed in and had less leverage to press an American agenda on the two most important issues: Iran and the Israeli-Palestinian negotiations.

The meetings in Israel with Prime Minister Netanyahu will go smoothly enough. President Obama will want to show the U.S.-Israeli relationship is strong and on track. It's an election year, America is focused largely on domestic issues and the Israelis have their own internal preoccupations with the military conscription issue. The reality is that there's no reason for any unpleasantness now, let alone a fight with Benjamin Netanyahu.

Yet, not too far below the surface, trouble is brewing. On Iran, Israel and America agree on the problem but not the solution; on the peace process, they differ on both the problem and the solution. And it may only be a matter of time before those differences grow more acute.

On Iran, Israel's worst fears are coming to pass. Secretary Clinton will try to reassure Netanyahu and urge patience, but her arguments will lack believability. Sanctions are painful but not nearly consequential enough to induce Iran to stop enrichment. P5+1 negotiations have now gone three rounds and seem directionless and without real prospects of success. The fact is that neither the mullahs nor the Obama administration is ready to risk a negotiated settlement. But both do have a common objective: stop Israel from attacking.

The Israelis will warn and rightly worry, and the Obama administration has no real answer as to how to stop Tehran's nuclear program from moving forward. Obama and Netanyahu share a similar assessment of the Iranian threat, but they clearly differ on the means and the timing to deal with it. The Israelis are on a much faster clock even though they know that a military strike will only delay Iran's program. "Mowing the grass," one Israeli conceded. And it will have to be cut again.

For the small power with the dark past, living on the knife's edge, an imperfect action is better than no action at all, particularly in the face of what the Israelis fear is an existential threat. Indeed, preemption—as messy as it's been—has almost always served Israel well. And besides, who knows, if Iran responds aggressively and/or overreacts, maybe the Americans will intervene and bring their formidable power to bear. You don't have to be a conspiracy theoriest to imagine that the Israelis would love to get Washington into this on their side. The Israelis will not act before the American elections unless Iran provokes them. But action is coming. The choice is between bombing and accepting the prospects of an Iranian bomb. And that may come to be America's choice as well. Obama has until November—then all bets are off. And neither Secretary Clinton nor the president himself will be willing or able to stop the Israelis should they decide to strike.

On the peace process, unlike Iran, the Americans and the Israelis disagree on both the problem and the solution. Obama thinks Netanyahu is withholding, more interested in settlements than a settlement with the Palestinians. Netanyahu is not prepared to offer terms Palestinians can accept and—psychologically and politically—isn't about to return to anything like the June 1967 borders or give up half of Jerusalem for a Palestinian capital. And those are the easy issues. On the matter of refugees, Netanyahu won't budge and in fact will demand that the Palestinians recognize Israel as the nation-state of the Jewish people.

Clinton, even if she were so inclined, has no leverage to push the Israelis. Forget that it's an election year and her boss's job is on the line, and consider the realities: a divided Fatah-Hamas Palestinian house; an Egyptian president from a party that regularly speaks about liberating Jerusalem; and a coalition agreement that binds the government to guidelines on the negotiations that no Palestinian can accept. These all provide enough talking points to kill any prospect of a serious negotiation.

As to settlements, the two sides will continue their passive-aggressive dance of agreeing to disagree. The recent recommendations of the Israeli government’s Levy committee to declare some settlements legal won't lead to anything more than dueling statements. Neither Israel nor the United States wants a crisis on this issue now. Hillary will protest, Bibi will defend and so will end yet another day in the ritualized tick-tock on this issue.

For now, both Iran and the peace process will be kicked down the road. Washington wants no quarrel before November elections. Indeed, there's no doubt that the institutional basis of Washington's ties with Jerusalem remains strong. The Obama administration can say without hesitation that it has worked to strengthen those ties, particularly from a security standpoint.

At the same time, the personal trust and sense of confidence between Obama and Netanyahu is pretty low. Dealing with Bibi is never easy (ask Bill Clinton). But unlike Obama, Clinton had an emotional connection to the idea of Israel and a bond with Israelis. Obama lacks both. Combine that with diverging views on what to do about the peace process and Iran, and you have a degree of separation we haven't seen in quite a while.

The United States and Israel will manage all that prospective complexity for now. But as American and Israeli perspectives diverge and Washington loses influence and clout in the region, Israel may well decide that it must increasingly act on its own. And there's no telling where that may lead.

Aaron David Miller is a Distinguished Scholar at the Woodrow Wilson Center. He served as an adviser to Republican and Democratic secretaries of state on Arab-Israeli negotiations.