In many developing countries, milk production varies greatly according to farm size, cattle breed, and milking practices. However, production systems often are dominated by smallholder farms. Therefore, relatively small volumes of milk are delivered daily from numerous farms to intermediate cooperatives which supply industrial units. This paper argues that in such two-stage dairy chains, milk quality could be improved by focusing on farming practices rather than on the testing of individual deliveries. Indeed, it is difficult to analyze their quality due to technical, economic, and logistic limitations. The objective of this study is to link on-farm practices with milk chemical quality parameters (fat and protein) and hygienic quality criteria (Aerobic Plate Count, APC and Coliforms). Cattle management practices were monitored monthly over one year on 23 farms located on an irrigation scheme in Morocco. 276 milk samples were analyzed. The monthly variability of milk quality parameters was then characterized. Results show that average cow milk chemical parameters vary within a normal range. They remain primarily linked to the genetic type of cows, the lactation stage, and the conversion of feed concentrates' net energy into milk. Overall milk hygienic quality was poor (APC and Coliforms counts were 100 fold international norms), due essentially to a lack of hygiene and inadequate milking conditions (hands, udder, and teat washing, type of bucket used, dirtiness of cows...). It is suggested that a close monitoring of herd management practices may allow the indirect control of milk quality parameters, thereby avoiding costly analyses of numerous smallholder milk deliveries.