Isolated populations that are geographically separated from the species’ contiguous range can be susceptible to threats, especially declining amphibians where early life stages are sensitive to changes in aquatic habitat. Assessing the biological, chemical, and physical attributes that indicate the extent of amphibian breeding and the quality of breeding ponds is essential but mostly unknown. The wood frog (Lithobates sylvaticus) is a glacial relict species found in two mountain ranges in Wyoming, USA. We assessed pond attributes that best explained the density of egg masses and late-stage tadpoles using water chemistry, algal biomass, benthic macroinvertebrates, and other physical characteristics in 15 ponds. Lower June phytoplankton biomass, higher pH, and an intermediate percent of emergent aquatic vegetation were associated with higher densities of egg masses; however, the intermediate density of very tolerant macroinvertebrates (tolerance ≥8) explained the most variation. We observed more tadpoles in ephemeral ponds compared to permanent ponds which explained the most variance; however, macroinvertebrate metrics explained little variation. Our study provides key information about habitat characteristics that best identify and measure the potential of breeding ponds for wood frogs. More broadly, our study contributes to understanding how aquatic invertebrates can help assess breeding habitat for amphibians.