The pathogenic fungus Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis in amphibians across the world, increasing the risk of population declines and species extinctions. Using a traditional sampling approach with traps, great crested newts (Triturus cristatus) and smooth newts (Lissotriton vulgaris) have been sampled in eight ponds for population estimates since 2013. The presence of Bd has been investigated by environmental DNA (eDNA) in the ponds since 2017, but results have often varied between sampling methods used during the same sampling period. By comparing results from pond water using two filter pore sizes (0.45 and 2.0 µm) and from amphibians (filtered bathwater, soft skin swabs, soft sandpaper rubbed on skin, and skin samples from between toes from toad carcasses), the results showed that filtered bathwater samples or gently rubbing amphibian skin with soft sandpaper are the most reliable methods for obtaining Bd DNA. Results from pond water filtered through the two pore sizes did not differ significantly across positive sites. Results also indicated that a variety of DNA concentrations should be tested in replicated qPCRs or ddPCRs to account for both potential inhibition and low levels of Bd DNA in the samples. Both crested newts and smooth newts were identified as infected with varying prevalence, but no trends in population declines were observed for any of the species during the sampling years 2013–2024. However, the number of crested newts in the monitoring ponds was altogether low and sometimes sporadic, and ponds with higher numbers of crested newts should be included in future studies on population trends in infected populations.