Personally, I believe that the most effective way to assess fluency is to assess reading comprehension. Both seem so interdependent that I cannot imagine separating the two.
If a student is given something to read on level, and is not only able to answer questions, but participate in dialogue, it would show that the student had excellent comprehension skills—and fluency in that he/she was able to express ideas and join in open discussion. Isn't the idea of fluency the ability to express one's ideas clearly and succinctly?
In Leslie Pepper's "Does Fluency Affect Comprehension," she writes:
...one of the primary goals of reading instruction should be to enhance fluency.
Fluency is defined in this article as...
...the ability to read aloud expressively and automatically with understanding.
Fluency makes for a better reader, and a better ready makes for a more effective problem-solver.
Comprehension strategies can be helpful, and there are many, but in that I'm pretty traditional, I favor the modeling format for students in all areas of study:
Instruction in comprehension strategy use often involves the gradual release of responsibility, wherein teachers initially explain and model strategies.
With practice, as students improve, teachers become less involved. It's like holding onto the seat of a bike until the child gains his/her balance, and then letting go. Improved reading comprehension gives students a sense of personal success and leads to improved fluency.