Salmon farming is threatened, economically and ecologically, by infectious diseases. To reduce the risk of epidemics, authorities have developed regulations. These are based on quantitative understanding of pathways of infection, representing disease specific risks. A stochastic model was fitted to historical data, to estimate risk factors associated with competing spread mechanisms. Three infectious diseases were compared, heart and skeletal muscle inflammation (HSMI), pancreas disease (PD) and infectious salmon anaemia (ISA). This study was based on space-time data, from Norway from 2003 to 2007, describing the susceptible fish cohorts and the reported infections. Particular interest was given to seaway distances between farms and their local management organisation. The parameter measuring the effect of distance to an infectious fish farm was positive and significant for all diseases, implying that the risk involved with proximate infectious fish farms increased with decreasing distance. For HSMI and PD there was a significant effect of sharing a contact network with an infectious farm. For HSMI, but not for PD or ISA, there was a significant effect of previous infected cohorts on the same farm. The relative contribution of each transmission pathway was dominated by seaway distance for PD and HSMI, while other non-defined pathways dominated for ISA. This comparative study highlights that the three diseases have different patterns of spread, with important consequences for disease prevention and management.