Bovine mammary gland inflammation, known as mastitis, is one of the most costly infectious diseases to the dairy industry. The goal of this research is to identify whether the environmental origin of milk microbiota influences milk biodiversity and mammary inflammation under different farm systems. To achieve this goal a cross-sectional survey was carried out on 3 dairy farms each using a different bedding type [straw (ST), Ssand, (SA) and recycled bedding material (RBM)]. To identify the diversity of microbiota in milk and in environmental sources, milk, teat-end swab and fecal samples were collected from each selected cow (n = 137), along with used bedding samples (n = 50) representative of each farm. Mammary gland inflammation was also estimated for each cow using milk somatic cell count (SCC). Using a Bayesian approach (SourceTracker), it was estimated that the overall environmental origin of the milk microbial communities (including teat-end, bedding and fecal sources) for farm RBM and farm SA was 47% and 43.5% respectively, while for farm ST was only 25%. Additional evidence of a difference in environmental contribution to milk between farms is that the bacterial diversity of milk was significantly different (and lower) than that of the teat-end for only farm ST (Shannon index, P < 0.05). In addition, farm ST had a lower bacterial diversity compared with farm RBM and SA (Shannon index, P < 0.05). Interestingly, both the proportion of milk microbiota originating from feces and the teat-end were positively correlated with milk bacterial diversity (Shannon index) (P < 0.01, r >0.39 for all farms). Meanwhile, the proportion of microbiota in milk originating from bedding only influenced milk bacterial diversity (Shannon index) for the RBM farm (r = 0.31, P < 0.05). While the proportion of microbiota from these sources was not correlated with milk SCC at the time of sampling (P > 0.05), milk bacterial diversity may be important to long-term stability of mammary inflammatory status. These results indicate that differences in milk biodiversity between farms is related to the level of microbiota originating from environmental sources such as bedding material.