The most immediate and dangerous effect to pesticide and fertilizer presence in your pond is fish death. Koi and other pond fish, while hearty, are extremely sensitive to water quality. A small amount of pesticide over spray from your garden or lawn can be all it takes to render your pond water uninhabitable. Absolute care must be taken to prevent seepage and over-spray of any chemical lawn or garden treatment.
Algae is a photosynthetic organism that behaves in much the same way a plant would. It requires sunlight and nutrients in the water for survival and can grow and reproduce rapidly when water conditions are favorable. Fertilizer presence in your pond can lead to what is called an algae bloom, or rapid algae growth. This will render your water a pea-soup green with a thick consistency and can kill fish and aquatic plants by reducing dissolved oxygen to dangerously low levels.
Aquatic plants use the water in a way similar to how terrestrial plants use soil. They absorb nutrients, as well as water, from your pond and use it in conjunction with photosynthesis. An aquatic plant in a pond with pesticides is like a terrestrial plant planted in soil with poison. Over spray or seepage from your garden or lawn fertilizers can be lethal to your aquatic plants.
Your pond does not have to be physically connected to other bodies of water to effect them, as well as the larger ecosystem surrounding your water feature. Birds landing near your pond and feeding on the seeds or shoots from your aquatic plants will ingest the chemicals and carry them to other parts of the environment. Your pond should be considered a part of the larger ecosystem and not thought of as separate or insulated from it.