Calf pre-weaning morbidity and mortality rates have been reported to be high in several countries. However, limited data have been reported on calf morbidity and mortality rates 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 enteropathogens causing diarrhea, failure of passive transfer of immunity, and poor colostrum quality in a sample of Australian dairy farms. One-hundred and 6 completed questionnaires and samples from 23 farms were analyzed (202 fecal, 253 calf serum, and 221 colostrum samples). Morbidity and mortality rates reported by farmers in pre-weaned heifers were 23.9% and 5.8%, respectively. These rates 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 true prevalence of 40.9% and 25.2%, respectively. Salmonella O-group D was the most prevalent at 67.9% of Salmonella-positive samples, followed by O-groups B (17.9%) and C (10.7%). Failure of passive transfer of immunity was observed in 41.9% of samples (mean herd 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 with regards to colostrum management and feeding hygiene.