Distributed data-intensive workflow applications are increasingly relying on and integrating remote resources including community data sources, services, and computational platforms. Increasingly, these are made available as data, SAAS, and IAAS clouds. The execution of distributed data-intensive workflow applications can exposé network bottlenecks between clouds that compromise performance. In this paper, we focus on alleviating network bottlenecks by using a proxy network. In particular, we show how proxies can eliminate network bottlenecks by smart routing and perform in-network computations to boost workflow application performance. A novel aspect of our work is the inclusion of multiple proxies to accelerate different workflow stages optimizing different performance metrics. We show that the approach is effective for workflow applications and broadly applicable. Using Montage1 as an exemplar workflow application, results obtained through experiments on Planet Lab showed how different proxies acting in a variety of roles can accelerate distinct stages of Montage. Our microbenchmarksalso show that routing data through select proxies can accelerate network transfer for TCP/UDP bandwidth, delay, and jitter, in general.