Gaffney joined the Bureau of Meteorology as a meteorological assistant in Perth in 1948 and moved to the Central Analysis Section in Head Office in Melbourne in 1960. In Melbourne, 1961-1964, he served as a senior meteorologist in the Hydrometeorological Section on rainfall maximisation and flood forecasting techniques, and was seconded to the Professional Officers' Association in 1963-1964 as Assistant General Secretary, where he acted as advocate in the Meteorologists' Arbitration Case (later the Scientists' Case). From the mid 1960s to the early 1980s Gaffney saw extensive service as a senior meteorologist in general and operational meteorological services, encompassing the organisation and provision of public weather, marine and climatological services. He expedited the preparation and publication of the Public Weather and Maritime Services Handbooks, and specialised in marine meteorology, particularly the development of marine weather services. From 1965 Gaffney coordinated the Climatic Survey Program to prepare approximately 100 climate surveys for planning, development and decentralisation in Australian climate districts. He was also project leader of the Climatic Atlas of Australia project. In the mid 1980s he transferred to the Bureau's National Climate Centre, where he was responsible for the issue of operational drought reviews and seasonal climate outlooks. Seasonal Climate Summaries for the Southern Hemisphere were prepared and published as a series in consecutive issues of the Australian Meteorological Magazine (1987-1991). Gaffney retired in 1991. His PhD thesis (1996) was a rigorous treatment of pastoral droughts in Australia in relation to the Southern Oscillation Index.