Aim: To investigate the spatial relationship between climate variability and cryptosporidiosis and giardiasis notifications in New Zealand between 1997 and 2006. Methods: Negative binomial regression was used to analyse spatial relationships between cryptosporidiosis and giardiasis notifications in New Zealand between 1997 and 2006, and climatological average rainfall and temperature at the Census Area Unit (CAU) level. The quality of domestic water supplies, urban-rural status and deprivation were included as covariates. Main results: Giardiasis: There was a positive association between rainfall and giardiasis and between temperature and giardiasis. Cryptosporidiosis: There was a positive association between rainfall and cryptosporidiosis and a negative association between temperature and cryptosporidiosis. The effect of rainfall was modified by the quality of the domestic water supply. Conclusions: These findings suggest that climate variability affects protozoan disease rates in New Zealand. However, predicting the effect of climate change from this study is difficult, as these results suggest that the projected increases in temperature and rainfall may have opposing effects on cryptosporidiosis rates. Nevertheless, water supply quality appeared to modify the impact of increased rainfall on cryptosporidiosis rates. This finding suggests that improving water supply quality in New Zealand could reduce vulnerability to the impact of climate change on protozoan diseases.