We relate discrepancy theory with the classic scheduling problems of minimizing max flow time and total flow time on unrelated machines. Specifically, we give a general reduction that allows us to transfer discrepancy bounds in the prefix Beck-Fiala (bounded iota 1-norm) setting to bounds on the flow time of an optimal schedule. Combining our reduction with a deep result proved by Banaszczyk via convex geometry, give guarantees of O(root logn) and O( root logn logp) for max flow time and total flow time, respectively, improving upon the previous best guarantees of O(logn) and O( log n log p). Apart from the improved guarantees, the reduction motivates seemingly easy versions of prefix discrepancy questions: any constant bound on prefix Beck-Fiala where vectors have sparsity two (sparsity one being trivial) would already yield tight guarantees for both max flow time and total flow time. While known techniques solve this case when the entries take values in {-1, 0, 1}, we show that they are unlikely to transfer to the more general 2-sparse case of bounded iota 1-norm.