Naturalism is the belief that all that exists in the universe is physical, material matter. There is no soul; we are just a complex collection of neurons. There is no Creator; there is evolution. And experiences like pain, pleasure, beauty, and a sense of self do not really exist. They are merely physiological reactions.
The philosophy of naturalism leads to several incomplete ways of thinking about the world. One of the most important concerns is the philosophy of telos, or purpose. The Christian worldview holds that the purpose of a thing must be given to it by a higher authority. Since naturalism teaches there is no higher authority (no deity), it deduces that mankind, creation, and individuals have no purpose in life.
Evolution, which the vast majority of naturalists believe, both supports the idea of having no purpose and tries to skirt around it. Naturalists believe that evolution explains how life on Earth came to be without the work of a supernatural element. But evolution also tries to return a sense of purpose to that life. Instead of mankind having an existential, spiritual purpose, evolution proposes that it is our genes which have a purpose—to propagate and multiply their genetic signature into the cosmos. This is not a true "purpose," however. Genes survive and multiply when and if conditions are right for them to do so. The "purpose" embodied by "survival of the fittest" comes down to dumb luck as much as any other element of evolution.
Naturalism, with its insistence that there is no soul, no mind, and no self, also teaches that there is no choice. Like the hurricane caused by the flap of a butterfly’s wings a half a world away, every impulse we have, every action we take, every word we say is determined by the events that came before. Whether or not we are controlled by our genes' drive to reproduce, we are incapable of choosing our beliefs, our worldview, or our favorite flavor of ice cream. This fatalistic philosophy becomes a problem in the realm of ethics; if our actions are out of our control, can criminals be held responsible for their crimes? It also reveals the hypocrisy of evolutionists who spew vitriol on creationists; if prior events determine our beliefs, how can theists be blamed for believing in God?
Naturalism also refers to a fairly benign methodology of research. Scientists, both atheistic and Christian, use naturalism to discover more about our world. It is the general assumption that everything has a physical or natural explanation, and investigating the natural elements will reveal that explanation. This is an advance on the pagan religions that taught that sex rituals would ensure a healthy harvest or that a black cat could cause bad luck. And it’s a rejection of the "God of the gaps" argument that says God is only involved in those things we cannot see or explain. The naturalistic methodology instead posits that, if we can’t explain something, we just haven't found the answer yet. It’s still an incomplete worldview, however. There is sufficient evidence that life could not have begun without outside interference. We can discover our world through the scientific method while still acknowledging the activity of a Creator.
It is true that our actions and beliefs are largely influenced by events we have been exposed to. That’s why God exhorts us to meditate on His Word (Deuteronomy 11:18) and keep our thoughts on things above (Colossians 3:2). The Bible also teaches that we have a distinct soul and spirit (Hebrews 4:12) and that mankind has a specific purpose (Genesis 1:26-31). In the end, naturalism is just a fancy way to deny the existence of God (Psalm 14:1).