Rainfall is not completely absent in desert areas, but it is highly variable. An annual rainfall of four inches is often used to define the limits of a desert. The impact of rainfall upon the surface water and groundwater resources of the desert is greatly influenced by landforms. Flats and depressions where water can collect are common features, but they make up only a small part of the landscape.

Arid lands, surprisingly, contain some of the world’s largest river systems, such as the Murray-Darling in Australia, the Rio Grande in North America, the Indus in Asia, and the Nile in Africa. These rivers and river systems are known as "exogenous" because their sources lie outside the arid zone. They are vital for sustaining life in some of the driest parts of the world. For centuries, the annual floods of the Nile, Tigris, and Euphrates, for example, have brought fertile silts and water to the inhabitants of their lower valleys. Today, river discharges are increasingly controlled by human intervention, creating a need for international river-basin agreements. The filling of the Ataturk and other dams in Turkey has drastically reduced flows in the Euphrates, with potentially serious consequences for Syria and Iraq.

The flow of exogenous rivers varies with the season. The desert sections of long rivers respond several months after rain has fallen outside the desert, so that peak flows may be in the dry season. This is useful for irrigation, but the high temperatures, low humidities, and different day lengths of the dry season, compared to the normal growing season, can present difficulties with some crops.

Regularly flowing rivers and streams that originate within arid lands are known as "endogenous." These are generally fed by groundwater springs, and many issue from limestone massifs, such as the Atlas Mountains in Morocco. Basaltic rocks also support springs, notably at the Jabal Al-Arab on the Jordan-Syria border. Endogenous rivers often do not reach the sea but drain into inland basins, where the water evaporates or is lost in the ground. Most desert streambeds are normally dry, but they occasionally receive large flows of water and sediment.

Deserts contain large amounts of groundwater when compared to the amounts they hold in surface stores such as lakes and rivers. But only a small fraction of groundwater enters the hydrological cycle—feeding the flows of streams, maintaining lake levels, and being recharged (or refilled) through surface flows and rainwater. In recent years, groundwater has become an increasingly important source of freshwater for desert dwellers. The United Nations Environment Programme and the World Bank have funded attempts to survey the groundwater resources of arid lands and to develop appropriate extraction techniques. Such programs are much needed because in many arid lands there is only a vague idea of the extent of groundwater resources. It is known, however, that the distribution of groundwater is uneven, and that much of it lies at great depths.

Groundwater is stored in the pore spaces and joints of rocks and unconsolidated (unsolidified) sediments or in the openings widened through fractures and weathering. The water-saturated rock or sediment is known as an "aquifer". Because they are porous, sedimentary rocks, such as sandstones and conglomerates, are important potential sources of groundwater. Large quantities of water may also be stored in limestones when joints and cracks have been enlarged to form cavities. Most limestone and sandstone aquifers are deep and extensive but may contain groundwaters that are not being recharged. Most shallow aquifers in sand and gravel deposits produce lower yields, but they can be rapidly recharged. Some deep aquifers are known as "fossil waters. The term "fossil" describes water that has been present for several thousand years. These aquifers became saturated more than 10,000 years ago and are no longer being recharged.

Water does not remain immobile in an aquifer but can seep out at springs or leak into other aquifers. The rate of movement may be very slow: in the Indus plain, the movement of saline (salty) groundwaters has still not reached equilibrium after 70 years of being tapped. The mineral content of groundwater normally increases with the depth, but even quite shallow aquifers can be highly saline.

沙漠中并不是完全没有降雨，只不过变数很大。通常年降水量100毫米以下是界定沙漠地区的条件。降水对沙漠地区地表和地下水资源的影响很大程度上取决于地貌。平原和洼地的共同特征是水源聚集，但是它们在地貌中所占比重很小。 令人惊奇的是，一些世界最大的河系都位于干旱地区，例如澳大利亚的墨累-达令河、北美洲的格兰德河、亚洲的印度河以及非洲的尼罗河。这些河流及河系因为源头位于干旱地区以外而被称为“外流河”。对世界上一些最干旱地区来说，它们哺育生命，意义重大。例如，几个世纪以来，尼罗河、底格里斯河和幼发拉底河每年都会泛滥洪水会为下游低洼地带的居民带来大量肥沃的泥沙和水源。现在，河水流量越来越多的受到人类的干预，因而有必要签署国际性的河流流域协议。阿塔图尔克大坝以及土耳其境内的其它大坝的蓄水极大地减少了幼发拉底河的径流量，可能会给叙利亚和伊拉克带来严重后果。 “外流河”的径流量通常受季节影响。雨季过后，从外部流入沙漠区域的长河可以持续好几个月，以便洪峰可以出现在旱季。这虽然利于灌溉，但是高温度、低湿度，加上旱季独特的昼长，相比正常生长季节依然很难种植一些农作物。 通常发源于干旱地区的河流和溪水被称为“内陆河”。它们主要是由地下水泉补给,很多出口来自石灰岩断层，例如摩洛哥的阿特拉斯山脉。玄武岩同样可以提供地下水泉，最具代表性的是约旦和叙利亚边界的Jabal Al-Arab河.内陆河通常都不能流入大海而是注入内陆盆,蒸发掉或者消失在地表。大多数沙漠河床通常都是干涸的，但偶有较大径流和沉积物。 相比于湖泊和河流等地表水，沙漠中地下水的贮藏量要大得多。不过只有一小部分地下水参与了水循环——补给河流径流量，维持湖泊水位，并通过地表径流和降雨进行再次补给（再注入）。近些年来，地下水作为沙漠住民的淡水来源，重要性日益突显。美国国家环境总署和世界银行开始拨款着手调查干旱地区的地下水资源并开发合适的开采技术。这些项目非常有必要，因为在很多干旱地区对于地下水资源的程度概念非常模糊。然而可以确定的是，地下水资源分布非常不均匀，且大部分埋藏较深。 地下水一般贮存于岩石孔隙、节理、松散沉积物或者断裂和风化作用形成的孔洞。饱含水的岩石或沉积物被称为“蓄水层”。因为沉积岩多孔，比如砂岩和砾岩，都是地下水的重要潜在源头。只要节理和裂缝扩大形成容器，石灰岩中也能够储存大量水资源。大部分石灰岩和砂岩蓄水层深广，但是储存的水资源不可再生。大多数沙石中较浅的蓄水层贮水量少，但可以迅速再生。一些深层地下水被称作“化石水”。用“化石”来形容水，这就意味着这些水已经存在了千年之久。这些蓄水层注满水起码已经1万年以上了，而其无法再生。 贮存在蓄水层的水并非不流动，而是会通过泉眼渗出或是进入其他蓄水层，可以流动水的比例可能很低：在印度河平原，流动的含盐地下水在开采了70年之后依旧不能达到平衡。正常情况下,地下水的矿物含量随着深度的增加而增加，，但是即使很浅的蓄水层中可能含盐量也很高。 阿特拉斯山脉（阿尔卑斯山系的一部分） 节理：岩石中的裂隙，其两侧岩石没有明显的位移。地壳上部岩石中最广泛发育的一种断裂构造。