This study quantifies the exposure of agricultural land in Aotearoa-New Zealand’s (A-NZ) flood hazard zones (FHZs). We developed a spatio-temporal flood exposure framework to quantify the extent of the area and yearly earnings before income and tax (EBIT) for arable, forestry, horticulture, sheep and beef, and dairy land in FHZs between 1990 and 2016. In 1990, ~1.57 million hectares of agricultural land were exposed, decreasing slightly to ~1.50 million hectares by 2016. However, there was a change in the lower-value types of agricultural land uses being exposed, such as for sheep and beef farming and forestry, toward dairy farming (from ~364,000 hectares in FHZs in 2008 to ~471,000 hectares in 2016). Dairy farming is more intensively staffed with larger amounts of fixed assets, making them less resilient to flood impacts. Despite this, conversion to dairy farming even within the identified FHZs has been driven by the increasing profitability of the enterprise. As a result of both the production value change and land area increases, the dairy EBIT values within FHZs rose rapidly from NZD 382 million to NZD 1.25 billion between 2008 and 2012, creating significantly more economic exposure for A-NZ. This trend is particularly evident in the Southland, Canterbury, and Waikato regions. Similarly, in the Marlborough, Tasman, and Hawke’s Bay regions, there was an increase in high-value horticultural land—predominantly viticulture—in FHZs (a increase of NZD 321 million in annual EBIT for exposed horticulture across the three regions). Identifying sub-national trends in agricultural flood exposure allows for a detailed analysis of the likely impacts in high-risk areas, which can inform emergency management plans and mitigative actions that diminish the economic impacts from flood events.