A habitat-based framework is a practical method for developing models (or, ecological production functions, EPFs) to describe the spatial distribution of ecosystem services. To generate EPFs for Yaquina estuary, Oregon, USA, we compared bird use patterns among intertidal habitats. Visual censuses were used to quantify abundance of bird groups and general species richness in: Zostera marina (eelgrass), Upogebia (mud shrimp)/mudflat, Neotrypaea (ghost shrimp)/sandflat, Zostera japonica (Japanese eelgrass), and low marsh estuarine habitats. Also assessed were (1) spatial variation within a habitat along the estuary gradient and, (2) temporal variation based on bi-monthly samples over a year at five tidal ranges. Z. marina was an important estuarine habitat based on nearly all metrics of bird use, except for shorebird densities. This suggests that reductions in native eelgrass habitat may reduce the abundance and diversity of birds in Yaquina estuary. Our results suggest that a habitat based assessment approach is generally feasible for developing relative EPFs related to the presence of birds within estuarine systems.