Oviposition site selection is critical for the reproductive success of oviparous organisms. We investigated oviposition site selection in three species of glass frogs—Espadarana prosoblepon, Hyalinobatrachium valerioi, and Teratohyla spinosa—in northeastern Costa Rica. We conducted nocturnal visual encounter surveys to estimate glass frog egg mass abundance and characterize oviposition site features in streams of three different habitats (pasture, secondary forest, and mature forest). Our results show differential oviposition site selection among all three species depending on vegetation and stream features. Hyalinobatrachium valerioi and T. spinosa, which oviposit almost exclusively on the underside of leaves, selected smooth leaves, while E. prosoblepon, which oviposits on the upper side of leaves or in moss, used moss eight times more than expected on the basis of availability. Hyalinobatrachium valerioi was found on larger leaves than T. spinosa and E. prosoblepon. Teratohyla spinosa and E. prosoblepon both oviposited most frequently above slow-moving water, while H. valerioi oviposited most frequently above fast-moving water. Espadarana prosoblepon was the only species affected by habitat type and had higher abundances of egg masses in mature forest than in secondary forest and pasture. Our results suggest that microhabitat plays a larger role in oviposition site selection than larger habitat classification. We propose that appropriate riparian microhabitat is a critical factor in sustaining glass frog populations in modified habitats and highlight the importance of preserving riparian corridors in altered landscapes.