Minimizing the application running cost becomes a must in our day when Cloud Computing offers support for a large variety of applications. Being at the confluence with Cyberinfrastructures and Big Data platforms, Cloud systems support efficient and effective workflows. Due to the increase in computational power for executing workflows, the need for efficient usage of said power also arises. After a brief overlook of current available workflow scheduling algorithms, such as HLFET -Highest Level First with Estimated Time or MCP -Modified Critical Path, it is clear that, for no specific constraints, they waste CPU resources, with no efficient task allocation. For this reason a new algorithm, called HER (Hybrid Algorithm for Workflow Scheduling in Cloud-based Cyberinfrastructures) is proposed in this paper. HER algorithm reduces CPU idle time, with effect on the number of wasted resources and ensure a good load balancing for a cluster of resources available in a Cloud environment. The HER algorithm is exemplified on a number of different workflow scenarios in CyberWater project -Prototype Cyberinfrastructure based System for Decision-Making Support in Water Resources Management. The experimental approach considers several workflows such as decision support, real-time alerts, and visualization that use computational, storage and network resources in Clouds.