Web design affects the successful deployment of search engine optimization. Web design that does not permit search engines the ability successfully follow all the links within a website is detrimental to the effectiveness of web design and being indexed properly with the search engines. Using too many images, scripting language and animation is one factor that will hinder your chances of being indexed properly.
For web design assistance and solutions try SEO, ecommerce and Web Design related sites. You will find fast and effective solutions to problems you are experiencing as well as art design tips.
One of the common instances of the inability of a web design not being search engine friendly is the use of JavaScript in the navigation systems or otherwise known as dynamic menus. Search engines cannot "read" this type of system, they are text based and can only "read", they do not parse, or think on a programming level. Therefore, the use of this scripting in the web design for navigation is not advisable. Not that you should avoid JavaScript, just do not use it as a navigational function.
If avoiding this type of navigation is not possible, then use some common work around. Such as providing alternate text links at the bottom or the pages, the use of the all-important sitemap is a great example of this search engine optimization strategy. This will allow the search engines to still find and index the pages that are in the menus where it does not see them and keep the page of indexing open.
Session controls such as Session ID's or "cookies" are another area that is a cause for concern, if your web design requires that these forms of tracking be required for search engines to crawl your site, it will prevent them from even looking. Search engines do not store "cookies", therefore if they are required the search engine just moves on to the next web site. For more information regarding cookies try this popular Cookie Central website.
Keep your content relevant and make sure that you leave options on all pages for the search engines to keep moving along, if they hit a roadblock, they will leave your site, regardless of the web design, or how well the site is search engine optimized.