Calf pre-weaning morbidity and mortality risks have been reported as high in several countries, with average values approximating 35% and 7%, respectively. However, limited data are available on calf morbidity and mortality risks in Australian dairy farms. The aims of this study were to (i) investigate current calf management practices on dairy farms in Australia and their association with herd-level morbidity and mortality using a questionnaire-based, cross-sectional study; and (ii) to estimate the prevalence of common enteropathogens causing diarrhea, the failure of passive transfer of immunity, and poor colostrum quality in a sample of Australian dairy farms. One-hundred and six completed questionnaires and samples from 23 farms were analyzed (202 fecal, 253 calf serum, and 221 colostrum samples). Morbidity and mortality risks reported by farmers in pre-weaned heifers were 23.8% and 5.6%, respectively. These risks were above the Australian Dairy Industry targets in 75.5% and 66.7% of respondents. The zoonotic pathogens Cryptosporidium spp. and Salmonella spp. were the most prevalent enteropathogens, with a true prevalence of 40.9% and 25.2%, respectively. Salmonella O-group D was present in 67.9% of Salmonella-positive samples, followed by O-groups B (17.9%) and C (10.7%). Failure of transfer of passive immunity (IgG < 10 g/L) was observed in 41.9% of calves (mean herd-level prevalence of 36.2%) and only 19.5% of colostrum samples met the standards of immunoglobulin content and microbiological quality. Collectively, these data indicate that there is still considerable room for improvement in calf rearing practices on Australian dairy farms, particularly in regard to colostrum management and feeding hygiene.