Using a query string inside of a clean url.

[eluser]Colin Williams[/eluser]

That means I’d have to know which of the URI parameters to grab.

Not necessarily. You could iterate over $this->uri->uri_to_assoc() and then it's dynamic.

Code:

$params = $this->uri->uri_to_assoc();
foreach ($params as $key => $value {
  $this->db->where($key, $value);
}

Just like you would iterate over the $_GET superglobal. There's no difference.