The DYRESM-CAEDYM model is a valuable tool for simulating water temperature for biochemical studies in aquatic ecosystem. The model requires inputs of surface short-wave radiation and long-wave radiation or total cloud cover fraction (TC). Long-wave radiation is often not measured directly so a method to determine TC from commonly measured short-wave solar irradiance (E(0)) and theoretical short-wave solar irradiance under a clear sky (Er) has broad application. A more than 17-year (15 November 1991 to 20 February 2009) hourly solar irradiance data set was used to estimate the peak solar irradiance for each ordinal date over one year, which was assumed to be representative of solar irradiance in the absence of cloud. Comparison between these daily observed values and the modelled clear-sky solar radiation over one year was in close agreement (Pearson correlation coefficient, r = 0.995 and root mean squared error, RMSE = 12.54 W m(-2)). The downloaded hourly cloudiness measurements from 15 November 1991 to 20 February 2009 was used to calculate the daily values for this period and then the calculated daily values over the 17 years were used to calculate the average values for each ordinal date over one year. A regression equation between (1 - E(0)/E(c)) and TC produced a correlation coefficient value of 0.99 (p > 0.01, n = 71). The validation of this cloud cover estimation model was conducted with observed short-wave solar radiation and TC at two sites. Values of TC derived from the model at the Lake Rotorua site gave a reasonable prediction of the observed values (RMSE = 0.10, r = 0.86, p > 0.01, a = 61). The model was also tested at Queenstown (South Island of New Zealand) and it provided satisfactory results compared to the measurements (RMSE = 0.16, r = 0.67, p > 0.01, n = 61). Therefore the model's good performance and broad applicability will contribute to the DYRESM-CAEDYM accuracy of water temperature simulation when long-wave radiation is not available. (C) 2010 Published by Elsevier Ltd.