Accurate knowledge of water content in seasonal snow can be helpful for water resource management. In this study, a distributed temperature index snow model based on temperature and precipitation as forcing data, is used to estimate snow storage in the Jollie catchment approximately 20km east of the main divide of the central Southern Alps, New Zealand. The main objective is to apply a frequently used assimilation method, the ensemble Kalman square root filter, to assimilate remotely sensed snow covered area into the model and evaluate the impacts of this approach on simulations of snow water equivalent. A 250m resolution remotely sensed data from Moderate Resolution Imaging Spectroradiometer (MODIS), specifically tuned to the study location was used. Temperature and precipitation were given on a 0.055 latitude/longitude grid. Precipitation was perturbed as input into the model, generating 100 ensemble members, which represented model error. Only observations of snow covered area that had less that 25% cloud cover classification were used in the assimilation precess. The error in the snow covered area observations was assumed to be 0.1 and grow linearly with cloud cover fraction up to 1 for a totally cloud covered pixel. As the model was not calibrated, two withholding experiments were conducted, in which observations withheld from the assimilation process were compared to the results. Two model states were updated in the assimilation, the total snow accumulation state variable and the total snow melt state variable. The results of this study indicate that the model underestimates snow storage at the end of winter and/or does not detect snow fall events during the ablation period. The assimilation method only affected simulated snow covered area and snow storage during the ablation period. That corresponded to higher correlation between modelled snow cover area and the updated state variables. Withholding experiments show good agreement between observations and simulated snow covered area. This study successfully applied the ensemble Kalman square root filter and showed its applicability for New Zealand conditions.