The development of efficient sampling protocols for the capture of environmental DNA (eDNA) could greatly help improve accuracy of occupancy monitoring for species that are difficult to detect. However, the process of developing a protocol in situ is complicated for rare species by the fact that animal locations are often unknown. We tested sampling designs in lake and stream systems to determine the most effective eDNA sampling protocols for two rare species: the Sierra Nevada yellow-legged frog (Rana sierrae) and the foothill yellow-legged frog (R. boylii). We varied water volume, spatial sampling, and seasonal timing in lakes and streams; in lakes we also tested multiple filter types. We found that filtering 2 L versus 1 L increased the odds of detection in streams 5.42X (95% CI: 3.2-9.19X) in our protocol, from a probability of 0.51 to 0.85 per technical replicate. Lake sample volumes were limited by filter clogging and we found no effect of volume or filter type. Sampling later in the season increased the odds of detection in streams by 1.96X for every 30 days (95% CI: 1.3 - 2.97X) but there was no effect for lakes. Spatial autocorrelation of the quantity of yellow-legged frog eDNA captured in streams between 100 and 200 m, indicating that sampling at close intervals is important.