The Neotropical otter (Lontra longicaudis) is listed as Near Threatened by the IUCN, which describes the standardization of field survey techniques and identification of key habitats as two research priorities. Basic ecological information such as habitat selection and diet is also lacking, especially in Central America. Using surveys for tracks and latrines from ten rivers on the Osa Peninsula of Costa Rica, we report results on habitat selection at the local and microhabitat scales, describe the general diet from 127 scats, and broadly discuss detection and general survey methods. We found that otters were positively associated with small-scale pastures surrounded by nearby forests at a local scale and/or negatively associated with densely forested areas. Otters further preferred deeper rivers at both local and microhabitat scales, while the availability of latrine substrates and sandbars was both important predictors of detection probability. We also deployed 12 camera traps to detect otters, and found they were much less efficient than sign surveys at determining occupancy, though our sample size is small. We conclude by proposing a methodology for standardized monitoring protocol using occupancy surveys which could be implemented across the Neotropical otter's range.