Although the effects of abiotic factors on species distributions and habitat selection have been widely investigated, studies have rarely succeeded at identifying the factors behind selection at the microhabitat level. Spider webs are extended phenotypes expected to be subject to fitness trade-offs. We tested the hypothesis that spiders with three-dimensional webs (tangle and sheet-and-tangle), which require more material to be built than two-dimensional orbicular webs, occupy microhabitats where they are better protected from strong rains. We show that tangle and sheet-and-tangle webs were indeed significantly more likely to be under immediate cover than expected by chance and than orb webs. Tangle webs occurred closest to the cover and were largely protected, whereas sheet-and-tangle webs, likely due to their larger size and mostly horizontal position, tended to be more exposed.  Sheet-and-tangle webs, however, occurred more often against tree trunks, where we show rain to be less intense. We further show that the proportion of 3D webs under immediate cover increased with annual precipitation along a dry to wet gradient in western Ecuador, an effect absent for 2D webs. The latter finding suggests that, in addition to using leaves for structural support, spiders with 3D webs seek microhabitat locations to shelter themselves from strong rains. Our findings illustrate how microhabitat selection may allow organisms to cope with abiotic factors at broader geographical scales, thus influencing organismal fitness and community structure.