Here is a web site from the state of Washington that is an excellent source for ID and cultural, mechanical and chemical management of aquatic weeds- Always be sure to check the label before making any pesticide applications:

http://www.ecy.wa.gov/programs/wq/plants/weeds/

Here is a publication from Aquatic Ecosystem Restoration Foundation which has alot of information on Best Mangement practices for Aquatic Weeds throughout the country

 Best Management Practices for Aquatic Weeds

Dr. Carole Lembi from Purdue University has several publications that cover many aspects of Aquatic weed control- here is one on Algae:

http://www.btny.purdue.edu/Pubs/APM/blue-green_factsheet.pdf

and one on general Aquatic Plant Mangement: 

http://www.ces.purdue.edu/extmedia/WS/WS_21.pdf