In high-elevation lakes of the Sierra Nevada (California), increases in P supply have been inferred from shifts in P to N limitation. To examine factors possibly leading to changes in P supply, we measured pools and transformations in soil P, and developed a long-term mass balance to estimate the contribution of parent material weathering to soil P stocks. Common Sierra Nevada soils were found to not be P-deficient and to be retentive of P due to the influence of Fe- and Al-oxides. Total P averaged 867 μg P g− 1 in the top 10 cm of soil (O and A horizons) and 597 μg P g− 1 in the 10–60 cm depth (B horizons), of which 70% in A horizons and 60% in B horizons was freely exchangeable or associated with Fe and Al. Weathering of parent material explained 69% of the P found in soils and lost from the catchment since deglaciation, implying that long-term atmospheric P deposition (0.02 kg ha− 1 yr− 1) represented the balance of P inputs (31%) during the past 10,000 years of soil development. During spring snowmelt ~ 27% of the total soil P was transferred between organic and inorganic pools; average inorganic P pools decreased by 232 μg P g− 1, while organic P pools increased by 242 μg P g− 1. Microbial biomass P was highest during winter and decreased six-fold to a minimum in the fall. Interactions between hydrology and biological processes strongly influence the rate of P transfer from catchment soils to lakes.