The major difference between natural and synthetic zeolite is time scale.
Natural zeolite take several days to create. while in laboratory we can synthesize zeolites from few hours to few days. Also pH and temperature is different in both cases.
Thus concept of reducing geological time scale to lab time scale is famous in zeolite synthesis.
As stated above, the main differences between natural and synthetic zeolites are the time scale in which they are produced, the amount of material that is produced and the quality of zeolites.
Natural zeolites have many more chemical elements in its structure that synthetic zeolites. Therefore, it is said that the synthetic zeolites are purer than natural zeolites. Natural zeolites are found in many geological environments and they have much greater structural and crystalchemical variability than synthetic zeolites. Also, natural zeolites occurr generally in large volumes in pyroclastic and sedimentary deposits. On the contrary, in the laboratory, synthetic zeolites of lower volumes are created.
Finally, synthetic zeolites are created in few hours or few days while natural zeolites can be generated in years or million years.
I am not sure, if the time scale is so much different. In respect to geological time scales the formation of zeolites in nature can be quite rapid.
As Francisco pointed out the major difference are the purity and the quantity. Natural zeolites which are used, are basically rocks that contain zeolites. On one hand the zeolites are never pure endmember phase, you can produce in the lab. On the other hand the rocks contain addition phases (like quartz, clays, calcite, glass, ....).
The big advantage of natural zeolites are the volume and quantity they can be mined in contrast to the low volumes you can produce in the lab.
The formal definition of a zeolite mineral (The Canadian Mineralogist Vol. 35, pp. 1571-1606 (1997) - see attached file) can help clarify the nature of natural zeolites. More information can certainly be gleaned from the literature cited in this article.
On the other hand there is no accepted official definition of a synthetic zeolite. The only guidance being the fact that the term usually refers to a synthetic material with zeolitic properties, i.e. a material with a crystal structure formed by a three-dimensional open framework of tetrahedra with inner channels and cavities providing the material with the capabilities of ion exchange and reversible dehydration. This sentence could in fact be taken as a rough definition of a synthetic zeolite but many are the synthetic compounds classified as zeolites with structural properties beyond this rather coarse definition.
Clearly a synthetic compound has a chemical composition made of the ingredients used in the synthesis, hence well known to the producer. The production of a synthetic zeolite is also aimed at providing the material with certain wanted properties i.e. it tends to be tailored to specific industrial needs. Whereas a natural zeolite is made of the most common mineral-forming elements and it’s composition may vary not only from a mineral species to another but also within the same mineral species as the attached publication clearly demonstrates.
More information about both, natural and synthetic zeolites can be found in the International Zeolite Association (IZA) web pages such as, for instance: http://www.iza-structure.org/databases/
I think they have no differences in essence.But the synthetic zeolites are designed by people especially some new zeolites. We made zeolites in a similar conditions with the formation of natural zeolites. So synthetic zeolites always are more perfect than natural zeolites.
I think the most important difference is the pore size distribution. Synthetic zeolites have a narrow pore size distribution due to the control of the ion exchange rate. for example you can produce 4A molecular sieve which its opening pores are about 4 angstrom and by replacing the Na+ with K+ the opening pore will be 3 angstrom.
Most of the natural zeolites are small pore. Variety of pore size we can get through synthesis. Apart from this purity is an another factor. Synthetic zeolites are more pure. Particle size also an another criteria. Natural zeolites are bulkier. etc.
Most of the zeolites found in nature are thermally stable. Some intermediate phases (meta stable) can not be found in nature, because their stability alters into the more stable one after passing the time or extended heating time. In laboratory one can tune mostly framework type desired for his application, in most of the cases one can also tune the chemical composition of the framework. The metastable zeolite growth can be achieved in the lab by quenching the synthesis reaction. But some of the zeolites are there they are synthesized in the laboratory very recently such as natrolite iin 2014. Apart from this the framework structure will be almost similar for natural and synthetic zeolite of same topology, and as a result of it nature of XRD pattern. Later can be different if one alters the chemical composition (shift in peak positions)... etc...
One more difference is there,, in laboratory on can synthesise the large amount of required zeolite while nature has limitations... so for industrial applications one can get bulk amount from pilot plants...