I will list and briefly explain a few things that affect and disrupt parts of the water cycle (hydrologic cycle). The items I list are not representative of all of the potential threats, though.
I'll start with an easy and obvious one. Climate change. I know it's all over the media right now as the bringer of all things evil, but climate change definitely affects the water cycle. The specific change that I am talking about is warmer average global temperatures. Warmer temperatures result in an increased amount of evaporation. Now I know what you might be thinking. "More water vapor in the air means more water to condense and eventually precipitate down. What's the disruption?" Warmer temperatures do increase evaporation rates, but warmer temperatures also allow the air to hold more water vapor before reaching saturation. The water will not condense as early as before, so it won't precipitate in the former regular pattern. That vapor might stay in the air much longer than normal. The atmosphere is not static, which means that vapor might be carried out of that particular ecosystem's water cycle.
Number 2. Part of the water cycle is runoff. The places and times that runoff occurs can be changed by human intervention. Modern day irrigation moves water hundreds of miles sometimes. Leeching and run off can occur along the way and at its final destination. It's possible that much water was never intended to occupy that particular area, so the run off portion of the water cycle is completely disrupted.
Number 3. Another part of the water cycle is called transpiration. Transpiration is evaporation out of plant leaves. All plants do it, but rain forests do it a lot. The transpired water goes into the atmosphere causing regions of localized high humidity. Because the air is always near the saturation point, it condenses often and precipitates right back down on the rain forest. It's a pretty cool cycle if you think about it. Without the trees to transpire water, there would be no water to rain down. Without the rain, there would be no trees. So what came first, the trees or the water?
I hope you see where I'm going with this. Deforestation projects get rid of the trees. No trees = no transpiration = decreased humidity = less rainfall. The region goes from a rain forest to a desert very quickly. Check out the map that I attached. Notice the latitude of the Sahara desert and the latitude of the rain forests of southeast Asia. Same latitude. So proximity to the equator doesn't mean desert dry or rain forest wet. It's the presence of the trees, and the water that they can capture and release. Here's a quote from "The Guardian" on the topic:
"As a result, the report notes, the deterioration of the rainforest – through logging, fires and land clearance – has resulted in a decrease in forest transpiration and a lengthening of dry seasons. This might be one of the factors of the severe drought affecting south-east Brazil. São Paulo – the biggest city in South America – is facing its worst water shortages in almost a century. October, which is usually the start of the rainy season, was drier than at any time since 1930, leaving the volume of the Cantareira reservoir system down to 5% of capacity."