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Agriculture is key to New Zealand's economy with land-use conversions in response to market forces occurring regularly, like that of recent dairy intensification throughout the country. However, land-use conversion can occasionally result in unexpected and significant consequences for public health that need to be accurately estimated and subsequently managed accordingly. For example, dairy cattle have high Giardia prevalence in New Zealand and identical strains from infected humans and cattle located in the same geographical region have recently been reported. Thus, the high rates of human infections in New Zealand compared to similar socioeconomic countries caused by the waterborne pathogen Giardia are particularly concerning given the increasing dairy cattle populations on the landscape. However, the ability of traditional, evidence-based, epidemiological approaches to detect such causal relationships between land-use and Giardia infections is limited given the many possible indirect links between the two, in turn highlighting the need to develop appropriate risk assessment techniques. As such, the general requirements for and development of risk assessment frameworks to evaluate the likelihood of public health risks from waterborne pathogens are introduced and explored using Giardia in New Zealand as an example. Specifically, the importance of recent advances in Giardia-based knowledge, the incorporation of such data into existing risk assessment frameworks and the influence of remaining research gaps are each discussed for expanding currently available risk assessment tools. Not surprisingly, the availability of appropriate risk assessment tools for agencies responsible for public health and environmental management would ensure the public health risks for Giardia resulting from land-use change could be quantified holistically and strategies subsequently developed through active agency communication to minimise such risks.