The bottom ice algae chlorophyll a (chl a)–snow depth (HS) relationship was investigated for first-year sea ice in Allen Bay, Nunavut, from 27 April to 13 June 2011. A transmitted irradiance technique was used to estimate ice algae chl a throughout the period at time series locations covered and cleared of snow. Furthermore, chl a was estimated along transects perpendicular to dominant snowdrift orientation, and at short-term snow clear experimental sites. The association between chl a and most snow depths was characterized by four phases over the spring; light limitation (negative relationship), a transitional period (no relationship), chl a decline associated with higher transmitted irradiance (positive relationship), and a final phase of chl a decline independent from HS (no relationship). Algal chl a under areas cleared of snow was lower, reached zero chl a earlier and declined faster than snow-covered control sites. Results indicated that snow removal caused these chl a responses through photoinhibition, as well as ice melt later in the spring. Based on this research we propose that weather events that can rapidly melt the snowpack could significantly deplete bottom ice chl a and cause early termination of the bloom if they occur late in the spring.